FSL expert,
I have just setup a new pc with ubuntu 16.04 LTS system and installed FSL 5.0.
But I encountered such error while running fslvbm_2_template -n:
600039015048_struc
600110937794_struc
600129552715_struc
600210241146_struc
600294620965_struc
600460215379_struc
600635899969_struc
600647003585_struc
Running segmentation: ID=30266
Running initial registration: ID=31661
Cannot open volume 600039015048_struc_GM_to_T for reading!
Cannot open volume template_4D_GM for reading!
ERROR: Could not open file
/usr/share/fsl/5.0/bin/fslswapdim: 107: [: =: unexpected operator
ERROR: Could not open file
/usr/share/fsl/5.0/bin/fslswapdim: 115: [: -gt: unexpected operator
ERROR: Could not open file
/usr/share/fsl/5.0/bin/fslswapdim: 117: [: -gt: unexpected operator
Cannot open volume template_GM for reading!
Cannot open volume template_GM for reading!
Creating first-pass template: ID=
/usr/share/fsl/5.0/bin/fsl_sub: 410: exit: Illegal number: -1
Running registration to first-pass template: ID=The command you have requested cannot be found or is not executable
/usr/lib/fsl/5.0/fsl_sub: 410: exit: Illegal number: -1
Creating second-pass template: ID=The command you have requested cannot be found or is not executable
Study-specific template will be created, when complete, check results with:
fslview struc/template_4D_GM
and turn on the movie loop to check all subjects, then run:
fslview /usr/share/fsl/5.0/data/standard/tissuepriors/avg152T1_gray struc/template_GM
to check general alignment of mean GM template vs. original standard space template.
I run fslvbm analysis successfully before on another server with Debian system. And I believe I strictly follow the steps in user guide on FSLwiki. I got the same error after several trials. So I am quite helpless on this issue so far.
Could anyone give a hit about how to solve this problem? Below is the data file in my FSL-VBM directory:
600039015048.nii.gz 600129552715.nii.gz 600294620965.nii.gz 600635899969.nii.gz slicesdir template_list
600110937794.nii.gz 600210241146.nii.gz 600460215379.nii.gz 600647003585.nii.gz struc
contents in template_list:
600039015048.nii.gz
600110937794.nii.gz
600129552715.nii.gz
600210241146.nii.gz
600294620965.nii.gz
600460215379.nii.gz
600635899969.nii.gz
600647003585.nii.gz
And file in struc after running fslvbm_2_bet -b -f 0.35
600039015048_struc_brain.nii.gz 600129552715_struc.nii.gz 600460215379_struc_brain.nii.gz 600647003585_struc.nii.gz
600039015048_struc.nii.gz 600210241146_struc_brain.nii.gz 600460215379_struc.nii.gz slicesdir
600110937794_struc_brain.nii.gz 600210241146_struc.nii.gz 600635899969_struc_brain.nii.gz
600110937794_struc.nii.gz 600294620965_struc_brain.nii.gz 600635899969_struc.nii.gz
600129552715_struc_brain.nii.gz 600294620965_struc.nii.gz 600647003585_struc_brain.nii.gz
I got the error after running: fslvbm_3_template -n
Thanks for reading my e-mail
Best,
Xin
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